src/gromacs/mdlib/calc_verletbuf.h

   1 /*
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  35
  36 #ifndef GMX_MDLIB_CALC_VERLETBUF_H
  37 #define GMX_MDLIB_CALC_VERLETBUF_H
  38
  39 #include "gromacs/utility/basedefinitions.h"
  40 #include "gromacs/utility/real.h"
  41
  42 struct gmx_mtop_t;
  43 struct t_inputrec;
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 typedef struct
  50 {
  51     int  cluster_size_i;  /* Cluster pair-list i-cluster size atom count */
  52     int  cluster_size_j;  /* Cluster pair-list j-cluster size atom count */
  53 } verletbuf_list_setup_t;
  54
  55
  56 /* Add a 5% and 10% rlist buffer for simulations without dynamics (EM, NM, ...)
  57  * and NVE simulations with zero initial temperature, respectively.
  58  * 10% should be enough for any NVE simulation with PME and nstlist=10,
  59  * for other settings it might not be enough, but then it's difficult
  60  * to come up with any reasonable (not crazily expensive) value
  61  * and grompp will notify the user when using the 10% buffer.
  62  */
  63 static const real verlet_buffer_ratio_nodynamics = 0.05;
  64 static const real verlet_buffer_ratio_NVE_T0     = 0.10;
  65
  66
  67 /* Sets the pair-list setup assumed for the current Gromacs configuration.
  68  * The setup with smallest cluster sizes is return, such that the Verlet
  69  * buffer size estimated with this setup will be conservative.
  70  * bSIMD tells if to take into account SIMD, when supported.
  71  * bGPU tells to estimate for GPU kernels (bSIMD is ignored with bGPU=TRUE)
  72  */
  73 void verletbuf_get_list_setup(gmx_bool                bSIMD,
  74                               gmx_bool                bGPU,
  75                               verletbuf_list_setup_t *list_setup);
  76
  77
  78 /* Calculate the non-bonded pair-list buffer size for the Verlet list
  79  * based on the particle masses, temperature, LJ types, charges
  80  * and constraints as well as the non-bonded force behavior at the cut-off.
  81  * If reference_temperature < 0, the maximum coupling temperature will be used.
  82  * The target is a maximum energy drift of ir->verletbuf_tol.
  83  * Returns the number of non-linear virtual sites. For these it's difficult
  84  * to determine their contribution to the drift exaclty, so we approximate.
  85  * Returns the pair-list cut-off.
  86  */
  87 void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
  88                              const t_inputrec *ir,
  89                              real reference_temperature,
  90                              const verletbuf_list_setup_t *list_setup,
  91                              int *n_nonlin_vsite,
  92                              real *rlist);
  93
  94 /* Struct for unique atom type for calculating the energy drift.
  95  * The atom displacement depends on mass and constraints.
  96  * The energy jump for given distance depend on LJ type and q.
  97  */
  98 struct atom_nonbonded_kinetic_prop_t
  99 {
 100     real     mass;     /* mass */
 101     int      type;     /* type (used for LJ parameters) */
 102     real     q;        /* charge */
 103     gmx_bool bConstr;  /* constrained, if TRUE, use #DOF=2 iso 3 */
 104     real     con_mass; /* mass of heaviest atom connected by constraints */
 105     real     con_len;  /* constraint length to the heaviest atom */
 106 };
 107
 108 /* This function computes two components of the estimate of the variance
 109  * in the displacement of one atom in a system of two constrained atoms.
 110  * Returns in sigma2_2d the variance due to rotation of the constrained
 111  * atom around the atom to which it constrained.
 112  * Returns in sigma2_3d the variance due to displacement of the COM
 113  * of the whole system of the two constrained atoms.
 114  *
 115  * Only exposed here for testing purposes.
 116  */
 117 void constrained_atom_sigma2(real                                 kT_fac,
 118                              const atom_nonbonded_kinetic_prop_t *prop,
 119                              real                                *sigma2_2d,
 120                              real                                *sigma2_3d);
 121
 122 #ifdef __cplusplus
 123 }
 124 #endif
 125
 126 #endif